Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

Simple item page
cg.authorship.typesCGIAR and advanced research institute
cg.contributor.affiliationUniversity of Maryland
cg.contributor.affiliationInternational Livestock Research Institute
cg.contributor.affiliationUniversity of Edinburgh
cg.contributor.affiliationUniversity of Basel
cg.contributor.affiliationWashington State University
cg.contributor.crpLivestock
cg.contributor.donorBill & Melinda Gates Foundation
cg.contributor.donorUnited States Department of Agriculture
cg.contributor.donorUnited States National Institute of Allergy and Infectious Diseases
cg.creator.identifierVishvanath Nene: 0000-0001-7066-4169
cg.creator.identifierRoger Pelle: 0000-0003-1053-085X
cg.creator.identifierRichard Bishop: 0000-0002-3720-9970
cg.creator.identifierClaudia Daubenberger: 0000-0001-7136-0642
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.1371/journal.pntd.0008781
cg.isijournalISI Journal
cg.issn1935-2735
cg.issue10
cg.journalPLOS Neglected Tropical Diseases
cg.reviewStatusPeer Review
cg.speciesTheileria parva
cg.subject.ilriANIMAL DISEASES
cg.subject.ilriBUFFALO
cg.subject.ilriCATTLE
cg.subject.ilriECF
cg.subject.ilriGENETICS
cg.subject.ilriLIVESTOCK
cg.volume14
dc.contributor.authorPalmateer, N.C.
dc.contributor.authorTretina, Kyle
dc.contributor.authorOrvis, J.
dc.contributor.authorIfeonu, O.O.
dc.contributor.authorCrabtree, J.
dc.contributor.authorDrabék, E.
dc.contributor.authorPelle, Roger
dc.contributor.authorAwino, Elias
dc.contributor.authorGotia, H.T.
dc.contributor.authorMunro, James B.
dc.contributor.authorTallon, L.
dc.contributor.authorMorrison, W.I.
dc.contributor.authorDaubenberger, C.A.
dc.contributor.authorNene, Vishvanath M.
dc.contributor.authorKnowles, Donald P.
dc.contributor.authorBishop, Richard P.
dc.contributor.authorSilva, Joana C.
dc.date.accessioned2020-11-03T21:20:45Zen
dc.date.available2020-11-03T21:20:45Zen
dc.identifier.urihttps://hdl.handle.net/10568/110042
dc.titleCapture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversityen
dcterms.abstractTheileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ~54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is ~20 kb larger than the genome from the reference, cattle-derived, Muguga strain, and contains 25 new potential genes. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average Wright’s fixation index (FST), genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species. These findings present clear implications for vaccine development, further demonstrated by the ability to assemble nearly all known antigens in the buffalo-derived strain, which will be critical in design of next generation vaccines. The DNA capture approach used provides a clear advantage in specificity over alternative T. parva DNA enrichment methods used previously, such as those that utilize schizont purification, is less labor intensive, and enables in-depth comparative genomics in this apicomplexan parasite.en
dcterms.accessRightsOpen Access
dcterms.audienceScientists
dcterms.available2020-10-29
dcterms.bibliographicCitationPalmateer, N.C., Tretina, K., Orvis, J., Ifeonu, O.O., Crabtree, J., Drabék, E., Pelle, R., Awino, E., Gotia, H.T., Munro, J.B., Tallon, L., Morrison, W.I., Daubenberger, C.A., Nene, V., Knowles, D.P., Bishop, R.P. and Silva, J.C. 2020. Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity. PLOS Neglected Tropical Diseases 14(10): e0008781.en
dcterms.issued2020-10-29
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherPublic Library of Science
dcterms.subjectcattleen
dcterms.subjectlivestocken
dcterms.subjectgenomicsen
dcterms.subjectinfectious diseasesen
dcterms.typeJournal Article

Files

License bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.75 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

ILRI articles in journals
CRP Livestock journal articles
ILRI animal and human health program outputs (2017–2024)